[gmx-users] Force equations of virtual site type 4fdn

Hi all-gmxers The force equations of old virtual site type 4fd were shown in GROMACS manual. But the ones of corresponding new type 4fdn are not shown in new GROMACS manual. Can someone do me a favor to give the force equations? Appreciate any help and thanks in advance! 2011-11-22 Best

[gmx-users] Gromacs-4.5.4 install error

Hi all gmx-users: I install gromacs-4.5.4, with tar xzf gromacs-4.5.4.tar.gz cd gromacs-4.5.4 export MPICC=/usr/mpi/gcc/mvapich2-1.4.1/bin/mpicc ./configure --prefix=/home/xuji/bin/gmx_4.5.4/parallel_float --enable-mpi --program-suffix=_mpi --without-x --with-fft=fftw3 --enable-all-static

[gmx-users] Problem about thread based MPI in Gromacs-4.5.1

Hi all In Gromacs-4.5 new features, there're "Running on a multi-core node now uses thread-based parallelization to automatically spawn the optimum number of threads in the default build. MPI is now only required for parallelization over the network. " And in Gromacs-4.5 manual, mdurn options h

[gmx-users] How to calculate the energy drift?

Hi all Gromacs users: In Gromacs 4 paper "GROMACS 4 Algorithms for Highly Efficient,Load-Balanced, and Scalable Molecular Simulation" "The energy drift for GROMACS is 0.01 kBT/ns per degree of freedom." But I don't know how to calculate the value of energy drift. Is this energy the kinetic ener

[gmx-users] How to update the neighbor list heuristically?

Hi all In GMX4 paper "GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation" VIII. Other New Features. It says that "Previously, GROMACS only supported neighbor list updates at fixed intervals, but the use of potentials that are switched exactly to zero a

[gmx-users] ra2max in nsc.c in Gromacs-4.0.7

Hi all GMX users The viriable ra2max in the file nsc.c of lines 608-637 seems not the maximun radii of all the atoms. Is it right? 2010-02-23 Best wishes！ Ji Xu The State Key Laboratory of Multiphase Complex System Institute of Process Engineering Chinese Academy of Sciences Beijing

[gmx-users] Does Gromacs support CHARMM force field now?

Hi all GMX users: I noticed that there're charmm27 force field files in Gromacs-4.0.5 software package. But charmm27 force field can't be choosed in pdb2gmx. So can I use charmm27 force field in Gromacs now? Thanks for any advice in advance! 2009-11-11 Ji Xu The State Key Laboratory of Mu

[gmx-users] Re: Re: Re: Re: Does GMX compute coulomb interaction between oxygen and hydrogen in SPC water model?

Hi Thank you for your advice and sorry for disturbing you agian. I read the cooresponding relevant manual sections, I've known how to get the parameters of the tabulated funcionns. But how much is the difference between the direct computation and the table lookup method is? For example, I simu

[gmx-users] Re: Re: Does GMX compute coulomb interaction between oxygen and hydrogen in SPC water model?

Thank you for your help! Mark Abraham. I make a mistake about the codes which compute the coulomb interactions in nb_generic.c yestoday. Sorry for it. And I find that there're some difference between the tabulated coulomb function and Vanilla cutoff coulomb interaction function. So waht does co

[gmx-users] Does GMX compute coulomb interaction between oxygen and hydrogen in SPC water model?

Hi all gromcas users: In SPC water model, it only has oxygen-oxygen VDW interactons. So is it the same with coulomb interatctions? Thanks for any advice in advance! 2009-10-24 Ji Xu The State Key Laboratory of Multiphase Complex System Institute of Process Engineering Chinese Academy of Sci

[gmx-users] How to add "an acetyl functional group" in the PDB file

2009-07-13 xuji ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the lis

[gmx-users] Continue run in Gromacs-4 with check point file

killed by signal 9 rank 6 in job 5 Node115_33001 caused collective abort of all ranks exit status of rank 6: killed by signal 9 Can someone help me with this problem? Appreciate any help in advance! Best wishes! 2009-03-2

[gmx-users] RE: RE: RE:RE: One question about Domain decomposition

e detail about the way you store the atoms of the chain molecule in Gromacs-4.0 in domain decomposition? And how the bonds, angles and dihedrals are reconstructed in each local domain? Best wishes! Xuji ___ gmx-users mailing listgmx-us

[gmx-users] RE:RE: One question about Domain decomposition

detail? Or give me a sketch map of your method? Thank you! Best wishes! xuji x...@home.ipe.ac.cn 　　2009-02-17 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/

[gmx-users] One question about Domain decomposition

ong how is the molecules' information stored in domain decomposition of Gromacs-4.0 ? Appreciate any help in advance! Best wishes! xuji x...@home.ipe.ac.cn 　　2009-02-16 ___ gmx-use

[gmx-users] Continue running in Gromacs 4.0

rong with my method and how can I continue a simulation in Gromacs-4.0? Appreciate any help in advance! xuji x...@home.ipe.ac.cn 　　2009-02-08 ___ gmx-users mailing listgmx-users@gr

[gmx-users] cCntinue running in Gromacs 4.0

got "No previous checkpoint file present, assuming this is a new run." So can someone tell me what's wrong with my method and how can I continue a simulation in Gromacs-4.0? Appreciate any help in advance! xuji x...@home.ipe.ac.cn 　　　

[gmx-users] Onw question about rlist rvdw rcoulomb and nstlist

ength of neighbour searching in Gromacs? Best wishes! 　　　　xuji x...@home.ipe.ac.cn 　　2009-01-09 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-

[gmx-users] One question in nb_generic.c file of Gromacs-4.0

dvance! 　　　　xuji [EMAIL PROTECTED] 　　2008-12-10 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don'

[gmx-users] Two questions about virial calculation

ibution to virial? Appreciate any help in advance! xuji [EMAIL PROTECTED] 　　2008-12-05 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/sear

[gmx-users] How to calculate the angle, dihedral and other contribution to virial

wishes! xuji [EMAIL PROTECTED] 　　2008-12-02 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.or

[gmx-users] RE:RE: How to calculate virial in gromacs-4.0? (xuji)

Hi Thank you for your explaination. But when I calculate the virial in all the inner force loops, the short range VDW and QQ force contribution to virial can be claculated straight forward. But when I claculate the bonded force, it seems difficult. Can you explain to me how to calculate the co

[gmx-users] How to calculate virial in gromacs-4.0?

some resoures about summing the virial with the periodic boundary condition? Appreciate any help in advance! Best wishes! 　　　　xuji [EMAIL PROTECTED] 　　2008-11-28 ___ gmx-users mailing

[gmx-users] Box vector shifts number in x and y/z dimension

! xuji [EMAIL PROTECTED] 　　2008-11-28 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don&#

[gmx-users] RE: How can I generate a Input *.gro file of coarse grain(xuji)

Program grompp, VERSION 3.3.3 Source code file: grompp.c, line: 469 Fatal error: number of coordinates in coordinate file (dppc_vesicle.gro, 72076) does not match topology (dppc_vesicle.top, 0) when I use grompp to generate the input file of mdrun. How can I solve these

[gmx-users] How can I generate a Input *.gro file of coarse grain model?

Dear all gromacs users: I am trying to use the MARTINI CG force field from Marrink et al. in my simulation. But I don't konw how to generate the input *.gro files. When I use all-atom model, in gromacs I can use "genbox" "editconf" et al to generate the input *.gro files. For example, I can use

[gmx-users] Cann't get the same result ?

Hi all: I run mdrun of gromacs-3.3.3 6 times of a small simulation, but I cann't get the same result every time. I run the mdrun program using "./mdrun -v -s md1.tpr -o md1.trr -c after_md1.gro -g md1.log -e md1.edr -x md1.xtc > md1.job && ./mdrun -v -s md1.tpr -o md1.trr -c after_md

[gmx-users] Asking help about PME

Hi all gromacs users: I am digging into the PME method in gromacs. Can someone tell me what files have something to do with PME and the corresponding method FFT? Thanks! 　　 Best wishes! Ji Xu Institute of Process Engineering Chinese Academy of Sciences P.O.Box 353, Beijing, 100080, China Tel